Re: [Joelib-devel] smarts

[Joerg K. W. <we...@in...>]

Hi naji,

so here are my guesses, no gurantee that the SMART patterns work. So 
please resend the tested/working patterns.

>>C= (participating in two fused benzene rings)
c~[#6]~c two benzene rings connected via aliphatic/aromatic via any bonds
or general aromatic rings ?
[r;a]~[#6]~[r;a]

>>C= (participating in two fused non-benzene rings)
[r;!a]~[#6]~[r;!a] two non-aromatic rings connected via 
aliphatic/aromatic via any bonds

>>C= (participating in two fused  rings: one benzene ring and one non-benzene ring)
[r;!a]~[#6]~[r;a]

> -CH=( participating in a benzene ring)
> 
>>C= (the formal double bond and a formal single bond participating in a benzene ring)
[#6,a,Q2,$(*-*),$(*=*)] so two heavy weight neighbors and neighbour 
environments with $(...), here general aromatic ring.
You can also work with hybridisation states using ^2, see 
joelib/data/plain/*.txt for examples

>>C= (two single bonds participating in a non- benzene ring)
with or without implicite hydrogens, so X or D or Q
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/functionalities/mol-smarts.html
and reference and link to daylight tutorial.
[#6,!a,r,Q2,$(*-*),$(*-*)] so two heavy weight neighbours, here general 
non-aromatic ring

> -CH=( participating in a non- benzene ring)
[#6,!a,r,Q2,$(*-*),$(*=*)]

>>C= (the formal double bond and a formal single bond participating in a non-benzene ring)
difference to -CH= ?

> =N- (participating in a ring )
[#7,r,Q2,$(*-*),$(*-*)] so assuming any ring, or only aliphatic ones ?

>>NH(participating in a ring )
[#7,r,H1,$(*-*),$(*-*)]

> -N< (participating in a ring )
> -N< (participating in two fused rings )
analogue to C, more or less.
> Any suggestions?
Yes :-)

> Thanks
Was me a pleasure.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
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